Small noncoding RNAs (sRNAs) have begun to rival transcriptional factors with regards to numbers and regulatory scope in gene expression. Most bacterial sRNAs regulate multiple mRNAs by short seed pairing, and it is now well-established that many govern large post-transcriptional regulons. We know little about how sRNAs differ from transcription factors in terms of regulatory activities and biological meaning, but increasing evidence suggests that they impact timing and threshold behaviour in gene expression programs.

This project aims to understand how sRNAs shape the dynamics of global responses in the pathogenic model organism, Salmonella Typhimurium. We will focus primarily on the SigmaE-induced envelope stress response, but also investigate the SOS response to DNA damage, the stringent response to starvation, and the regulatory cascades that induces Salmonella’s genes for host cell invasion.

We will harness the power of RNA deep sequencing and in vivo cross-linking for genome-wide profiling of regulation at the levels of DNA and RNA in parallel. This will unravel temporal and directional differences in the regulation of individual genes at the transcriptional versus post-transcriptional level, and identify network motifs that interconnect these two layers in natural systems. Knowledge of these motifs will feed into a rational design of sRNAs that function as timing devices in synthetic control circuits.

... coming soon

Förstner KU, Vogel J, Sharma CM (2014) READemption - A tool for the computational analysis of deep-sequencing-based transcriptome data. Bioinformatics. [Epub ahead of print]

Sharma CM, Vogel J (2014). Differential RNA-seq: the approach behind and the biological insight gained. Curr Opin Microbiol 19:97-105. 

Eulalio A, Schulte L, Vogel J (2012). The mammalian microRNA response to bacterial infections. RNA Biol 9(6):742-50.

Papenfort K, Vogel J (2014). Small RNA functions in carbon metabolism and virulence of enteric pathogens. Front Cell Infect Microbiol 4:91.

Saliba AE, Westermann AJ, Gorski SA, Vogel J (2014). Single-cell RNA-seq: advances and future challenges. Nucleic Acids Res 42(14):8845-60.

Fröhlich KS, Papenfort K, Fekete A, Vogel J (2013). A small RNA activates CFA synthase by isoform-specific mRNA stabilization. EMBO J 32(22):2963-79.

Heidrich N, Vogel J (2013). Same same but different: new structural insight into CRISPR-Cas complexes. Mol Cell 52(1):4-7.

Heidrich N, Vogel J (2013). CRISPRs extending their reach: prokaryotic RNAi protein Cas9 recruited for gene regulation. EMBO J 32(13):1802-4.

Holmqvist E, Vogel J (2013). A small RNA serving both the Hfq and CsrA regulons. Genes Dev 27(10):1073-8. 

Papenfort K, Sun Y, Miyakoshi M, Vanderpool CK, Vogel J (2013). Small RNA-mediated activation of sugar phosphatase mRNA regulates glucose homeostasis. Cell 153(2):426-37. 

Vogel J, Luisi BF (2011)

Hfq and its constellation of RNA

Nature Reviews Microbiology 9(8):578-89

Deltcheva E, Chylinski K#, Sharma CM#, Gonzales K, Chao Y, Pirzada ZA, Eckert MR, Vogel J, Charpentier E (2011)

CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III

Nature 471(7340):602-7

Schulte LN, Eulalio A, Mollenkopf HJ, Reinhardt R, Vogel J (2011)

Analysis of the host microRNA response to Salmonella uncovers the control of major cytokines by the let-7 family

EMBO J 30(10):1977-89

Sharma CM, Hoffmann S, Darfeuille F, Reignier J, Findeiß S, Sittka A, Chabas S, Reiche K, Hackermüller J, Reinhardt R, Stadler PF, Vogel J (2010)

The primary transcriptome of the major human pathogen Helicobacter pylori

Nature 464(7286):250-5

Papenfort K#, Bouvier M#, Mika F#, Sharma CM, Vogel J (2010)

Evidence for an autonomous 5’ target recognition domain in an Hfq-associated small RNA

PNAS 107(47):20435-40

Pfeiffer V, Papenfort K, Lucchini S, Hinton JC, Vogel J (2009)

Coding sequence targeting by MicC RNA reveals bacterial mRNA silencing downstream of translational initiation

Nature Structural & Molecular Biology 16(8):840-846

Bouvier M, Sharma CM, Mika F, Nierhaus KH, Vogel J (2008)

Small RNA binding to 5’ mRNA coding region inhibits translational initiation

Molecular Cell 32(6):827-37

Urban JH, Vogel J (2008)

Two seemingly homologous noncoding RNAs act hierarchically to activate glmS mRNA translation

PLoS Biology 6(3):e64

Sittka A, Lucchini S, Papenfort K, Sharma C, Rolle K, Binnewies TT, Hinton JC, Vogel J (2008)

Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq

PLoS Genetics 4(8):e1000163

Sharma CM, Darfeuille F, Plantinga T, Vogel J (2007)

A small RNA regulates multiple ABC transporter mRNAs by targeting C/A-rich elements inside and upstream of ribosome binding sites

Genes & Development 21(21):2804-2817